annotate macros.xml @ 9:ec9cbd6b9a49 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
author iuc
date Fri, 15 Jan 2021 17:39:11 +0000
parents 00fbfac99d39
children a6fba3d92531
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1 <macros>
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2 <!-- REMEMBER to bump the version of rna_star_index_builder_data_manager
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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3 whenever you make changes to the following two version tokens!
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178bdbdb6d24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 57f71aa633a43ab02bbf05acd0c6d7f406e01f1e"
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4 The data manager uses a symlink to this macro file to keep the STAR and
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5 the index versions in sync, but you should manually adjust the +galaxy
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6 version number. -->
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7 <!-- STAR version to be used -->
9
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8 <token name="@VERSION@">2.7.7a</token>
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9 <!-- STAR index version compatible with this version of STAR
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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10 This is the STAR version that introduced the index structure expected
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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11 by the current version.
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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12 It can be found for any specific version of STAR with:
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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13 STAR -h | grep versionGenome
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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14 or by looking for the versionGenome parameter in source/parametersDefault
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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15 of STAR's source code -->
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16 <token name="@IDX_VERSION@">2.7.4a</token>
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17 <token name="@IDX_DATA_TABLE@">rnastar_index2x_versioned</token>
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e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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19 <xml name="requirements">
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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20 <requirements>
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21 <requirement type="package" version="@VERSION@">star</requirement>
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22 <requirement type="package" version="1.9">samtools</requirement>
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23 <yield />
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24 </requirements>
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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25 </xml>
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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26
8
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27 <xml name="edam">
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28 <edam_topics>
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29 <edam_topic>topic_3170</edam_topic>
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30 <edam_topic>topic_3308</edam_topic>
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31 </edam_topics>
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32 <edam_operations>
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33 <edam_operation>operation_0292</edam_operation>
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34 </edam_operations>
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35 </xml>
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ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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36
1
e613048778d9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 2911002ccd79fe062f6346ee5699ea262f92f04f"
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37 <xml name="index_selection" token_with_gene_model="0">
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38 <param argument="--genomeDir" name="genomeDir" type="select"
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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39 label="Select reference genome"
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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40 help="If your genome of interest is not listed, contact the Galaxy team">
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41 <options from_data_table="@IDX_DATA_TABLE@">
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42 <filter type="static_value" column="4" value="@WITH_GENE_MODEL@" />
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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43 <filter type="static_value" column="5" value="@IDX_VERSION@" />
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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44 <filter type="sort_by" column="2" />
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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45 <validator type="no_options" message="No indexes are available for the selected input dataset" />
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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46 </options>
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47 </param>
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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48 </xml>
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49
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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50 <token name="@FASTQ_GZ_OPTION@">
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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51 --readFilesCommand zcat
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52 </token>
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53 <xml name="citations">
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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54 <citations>
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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55 <citation type="doi">10.1093/bioinformatics/bts635</citation>
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56 </citations>
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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57 </xml>
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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58 <xml name="@SJDBOPTIONS@" token_optional="true">
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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59 <param argument="--sjdbGTFfile" type="data" format="gff3,gtf" label="Gene model (gff3,gtf) file for splice junctions" optional="@OPTIONAL@" help="Exon junction information for mapping splices"/>
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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60 <param argument="--sjdbOverhang" type="integer" min="1" value="100" label="Length of the genomic sequence around annotated junctions" help="Used in constructing the splice junctions database. Ideal value is ReadLength-1"/>
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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61 </xml>
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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62 <xml name="dbKeyActions">
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63 <actions>
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64 <conditional name="refGenomeSource.geneSource">
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65 <when value="indexed">
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66 <action type="metadata" name="dbkey">
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67 <option type="from_data_table" name="@IDX_DATA_TABLE@" column="1" offset="0">
0
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68 <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
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69 <filter type="param_value" ref="refGenomeSource.GTFconditional.genomeDir" column="0"/>
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70 </option>
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71 </action>
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72 </when>
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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73 <when value="history">
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74 <action type="metadata" name="dbkey">
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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75 <option type="from_param" name="refGenomeSource.genomeFastaFiles" param_attribute="dbkey" />
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76 </action>
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77 </when>
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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78 </conditional>
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79 </actions>
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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80 </xml>
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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81 <token name="@TEMPINDEX@"><![CDATA[
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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82 ## Create temporary index for custom reference
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
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83 #if str($refGenomeSource.geneSource) == 'history':
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
84 mkdir -p tempstargenomedir &&
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
85 STAR
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
86 --runMode genomeGenerate
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
87 --genomeDir 'tempstargenomedir'
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
88 --genomeFastaFiles '${refGenomeSource.genomeFastaFiles}'
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
89 ## Handle difference between indices with/without annotations
7
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 6
diff changeset
90 #if 'GTFconditional' in $refGenomeSource:
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 6
diff changeset
91 ## GTFconditional exists only in STAR, but not STARsolo
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 6
diff changeset
92 #if str($refGenomeSource.GTFconditional.GTFselect) == 'with-gtf':
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 6
diff changeset
93 --sjdbOverhang '${refGenomeSource.GTFconditional.sjdbOverhang}'
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 6
diff changeset
94 --sjdbGTFfile '${refGenomeSource.GTFconditional.sjdbGTFfile}'
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 6
diff changeset
95 #if str($refGenomeSource.GTFconditional.sjdbGTFfile.ext) == 'gff3':
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 6
diff changeset
96 --sjdbGTFtagExonParentTranscript Parent
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 6
diff changeset
97 #end if
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 6
diff changeset
98 #end if
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 6
diff changeset
99 #else:
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 6
diff changeset
100 ## ref genome selection is less complex for STARsolo cause
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 6
diff changeset
101 ## with-gtf is mandatory there
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 6
diff changeset
102 --sjdbOverhang '${refGenomeSource.sjdbOverhang}'
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 6
diff changeset
103 --sjdbGTFfile '${refGenomeSource.sjdbGTFfile}'
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 6
diff changeset
104 #if str($refGenomeSource.sjdbGTFfile.ext) == 'gff3':
0
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
105 --sjdbGTFtagExonParentTranscript Parent
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
106 #end if
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
107 #end if
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
108 #if str($refGenomeSource.genomeSAindexNbases):
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
109 --genomeSAindexNbases ${refGenomeSource.genomeSAindexNbases}
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
110 #end if
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
111 --runThreadN \${GALAXY_SLOTS:-4}
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
112 &&
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
113 #end if
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
114 ]]></token>
2
3a1253ee137b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
iuc
parents: 1
diff changeset
115 <token name="@REFGENOMEHANDLING@" ><![CDATA[
0
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
116 --runThreadN \${GALAXY_SLOTS:-4}
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
117 --genomeLoad NoSharedMemory
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
118 --genomeDir
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
119 #if str($refGenomeSource.geneSource) == 'history':
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
120 tempstargenomedir
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
121 #else:
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
122 '${refGenomeSource.GTFconditional.genomeDir.fields.path}'
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
123 ## Handle difference between indices with/without annotations
2
3a1253ee137b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit ce3f681beac515bc20661e790c2b326077f853ba"
iuc
parents: 1
diff changeset
124 #if str($refGenomeSource.GTFconditional.GTFselect) == 'without-gtf':
0
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
125 #if $refGenomeSource.GTFconditional.sjdbGTFfile:
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
126 --sjdbOverhang $refGenomeSource.GTFconditional.sjdbOverhang
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
127 --sjdbGTFfile '${refGenomeSource.GTFconditional.sjdbGTFfile}'
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
128 #if str($refGenomeSource.GTFconditional.sjdbGTFfile.ext) == 'gff3':
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
129 --sjdbGTFtagExonParentTranscript Parent
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
130 #end if
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
131 #end if
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
132 #end if
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
133 #end if
e3c94e2933c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 686574b0392e554b75035a9b79bc919dfda9ab97"
iuc
parents:
diff changeset
134 ]]></token>
9
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
135 <token name="@READSHANDLING@" ><![CDATA[
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
136 ## Check that the input pairs are of the same type
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
137 ## otherwise STARsolo will run for a long time and then error out.
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
138 ## We consume either repeats of two inputs R1 + R2
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
139 ## or a collection of paired reads.
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
140 #if str($sc.input_types.use) == "repeat":
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
141 #set $reads1 = []
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
142 #set $reads2 = []
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
143 #for $r1, $r2 in zip($sc.input_types.input1, $sc.input_types.input2):
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
144 #assert $r1.datatype == $r2.datatype
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
145 #silent $reads1.append(str($r1))
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
146 #silent $reads2.append(str($r2))
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
147 #end for
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
148 #set $reads1 = ','.join($reads1)
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
149 #set $reads2 = ','.join($reads2)
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
150 #elif str($sc.input_types.use) == "list_paired":
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
151 #set $r1 = $sc.input_types.input_collection.forward
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
152 #set $r2 = $sc.input_types.input_collection.reverse
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
153 #set $reads1 = $r1
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
154 #set $reads2 = $r2
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
155 #end if
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
156 ## cDNA sequence(s) [R2] always go first, then barcode(s) [R1]
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
157 ## see: Section 3.2 of STAR manual for multiple inputs, and Section 13 for STARsolo inputs
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
158 --readFilesIn $reads2 $reads1
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
159 --soloCBmatchWLtype $sc.soloCBmatchWLtype
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
160 #if $r1.is_of_type('fastq.gz', 'fastqsanger.gz'):
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
161 @FASTQ_GZ_OPTION@
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
162 #end if
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
iuc
parents: 8
diff changeset
163 ]]></token>
7
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 6
diff changeset
164 <xml name="ref_selection">
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 6
diff changeset
165 <param argument="--genomeFastaFiles" type="data" format="fasta" label="Select a reference genome" />
e403d27e8f24 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit a8e319862d723654c372a6d71e5de76e052586a9"
iuc
parents: 6
diff changeset
166 <!-- Currently, this parameter is not exposed in the wrapper,
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167 but used only in the tests to avoid excessive index sizes for
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168 the tiny test genomes. -->
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169 <param name="genomeSAindexNbases" type="hidden" value="" />
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170 </xml>
0
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171 <xml name="stdio" >
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172 <stdio>
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173 <regex match="FATAL error" source="both" level="fatal"/>
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174 <regex match="EXITING: FATAL INPUT ERROR:" source="both" level="fatal"/>
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175 <regex match="EXITING: fatal error trying to allocate genome arrays, exception thrown: std::bad_alloc" source="both" level="fatal"/>
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176 <regex match="\[sam_read1\] missing header\? Abort!" source="both" level="fatal"/>
2
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177 <yield />
0
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178 </stdio>
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179 </xml>
9
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180 <xml name="input_selection">
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181 <conditional name="input_types" >
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182 <param name="use" type="select" label="Input Type" >
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183 <option value="repeat" >Separate barcode and cDNA reads</option>
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184 <option value="list_paired" >Paired collection of barcode and cDNA reads</option>
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185 </param>
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186 <when value="repeat">
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187 <param format="fastq,fasta,fastq.gz,fastqsanger.gz" name="input1" type="data" multiple="true"
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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188 label="RNA-Seq FASTQ/FASTA file, Barcode reads" />
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189 <param format="fastq,fasta,fastq.gz,fastqsanger.gz" name="input2" type="data" multiple="true"
ec9cbd6b9a49 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/rgrnastar commit 00c545ddbf0f008903f4b4c11d476e6089c3f531"
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190 label="RNA-Seq FASTQ/FASTA file, cDNA reads"/>
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191 </when>
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192 <when value="list_paired">
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193 <param name="input_collection" collection_type="paired" type="data_collection" format="fastq,fasta,fastq.gz,fastqsanger.gz" label="Collection of Pairs" />
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194 </when>
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195 </conditional>
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196 </xml>
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197 <xml name="input_selection_smart_seq">
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198 <conditional name="input_types_smart_seq" >
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199 <param name="use" type="select" label="Input Type" >
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200 <option value="list_single_end" >Single-end FASTQ collection</option>
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201 <option value="list_paired_end" >Paired FASTQ collection</option>
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202 </param>
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203 <when value="list_single_end">
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204 <param name="single_end_collection" collection_type="list" type="data_collection" format="fastq,fasta,fastq.gz,fastqsanger.gz" label="List of single-end FASTQ files" />
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205 </when>
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206 <when value="list_paired_end">
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207 <param name="paired_end_collection" collection_type="list:paired" type="data_collection" format="fastq,fasta,fastq.gz,fastqsanger.gz" label="List of paired-end FASTQ files" />
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208 </when>
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209 </conditional>
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210 </xml>
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211 <xml name="umidedup_options">
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212 <option value="1MM_All" selected="true">All</option>
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213 <option value="1MM_Directional" >Directional</option>
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214 </xml>
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215 <xml name="anchor_types">
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216 <option value="0">Read start</option>
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217 <option value="1">Read end</option>
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218 <option value="2">Adapter start</option>
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219 <option value="3">Adapter end</option>
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220 </xml>
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221 <xml name="cb_match_wl_common">
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222 <option value="Exact" >Exact</option>
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223 <option value="1MM" >Single match</option>
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224 </xml>
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225 <xml name="cb_match_wl_cellranger">
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226 <option value="1MM_multi" selected="true" >Multiple matches (CellRanger 2)</option>
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227 <option value="1MM_multi_pseudocounts" >Multiple matches (CellRanger 3)</option>
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228 </xml>
0
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229 </macros>